Joel, I think most people on this list at one time or another have shared your experience of wanting to throw the towel in due to frustration, when I succumb to the effect's I usually just step away for a day or two and give it a bit of thought, plus a few beers.

I dont mean to insult you but what works good for me is that I go back and check all the basic's, top dead center on #1, timing marks all ligned up etc etc, making sure the fit and function make sense, and I'm comfortable with what I see, having a extra wire hanging about that I'm not all that sure of ( function wise ) would give me pause for concern.

And one last thought, are your grounding straps / wires making a good contact, not sure about the Petronix but my Alison was giving me trouble due to a bad ground.